Gromacs 5.1 has been installed on Oakley; usage is via the module gromacs/5.1. For information on available executables and installation details see the software page for Gromacs or the output of the respective module help command, e.g.: module help gromacs/5.1.
The OSCMatlabPCT, the package used for configuring and submitting parallel MATLAB jobs, was updated on Sep. 17, 2015. This is because after Downtime two config files cannot be recognized (format error) by clusters.
The cuda/4.1.28 module was removed from Oakley during the software update. It has been restored because it is required for amber/11.
The default modules of some pacakges were updated on Oakley. Users who have built their own software may be required to rebuild their software or explicitly load the compiler and MPI modules used in building the software. For more details, see Updates to Oakley Application Softwar
ParMETIS (Parallel Graph Partitioning and Fill-reducing Matrix Ordering) is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes developed in Karypis lab.
METIS (Serial Graph Partitioning and Fill-reducing Matrix Ordering) is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes developed in Karypis lab.
Connections to OSC
In order for users to access OSC resources through the web your firewall rules should allow for connections to the following IP ranges. Otherwise, users may be blocked or denied access to our services.
The followingg TCP ports should be opened:
- 80 (HTTP)
- 443 (HTTPS)
- 22 (SSH)
The following domain should be allowed:
Blast version 2.2.31+ is now installed on Oakley.
SuperLU_MT 3.0 and SuperLU_DIST 4.1 have been installed on Oakley. They are available for use with the Intel 15, gnu 5, and PGI 15 compilers.